RetrogeneDB ID: retro_mtru_1

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 4:42136223..42137288(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_4g101860
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_3g070000
• Aliases: None
• Description: None

Sequence

>retro_mtru_1
ATGGTGGAAGCACAAACATGGACAACAAGAAGAATGAGCAACCCAAGATTACACACATTAGACACAAACGACCAATTACA
ATTAGACATACCACAAACACCACCAAGTGACCAAAGAAACAATGGATCCAACATCAACAACAACAACCTAGTAACAACTT
CACTTATAATAGCATCATGGTATTTTTCAAACATAGGTGTTCTTCTCTTAAACAAATATCTTTTAAGTTTCTACGGTTAC
CGTTACCCTATTTTTCTTACAATGCTTCACATGCTATCTTGCGCCGCTTATTCCTACGCCGCCATTAACGTTGTTCAGTT
TGTTCCTTATCAACAAATCCACTCCAAAAAACAGTTTCTGAAAATATTTGCTCTTAGCGCAATTTTCTGCTTCTCAGTTG
TTTGTGGAAATACCTCATTGAGATATTTACCTGTTTCTTTTAACCAAGCTATTGGTGCAACCACACCATTTTTCACCGCG
ATTTTCGCGTTTTTGATTACTTGTAAAAAAGAAACTGCTGAGGTTTATCTTGCTTTGTTACCAGTGGTGTTAGGGATTGT
TGTTTCAACAAATAGTGAACCTTTGTTTCATTTGTTTGGGTTTTTGGTTTGTGTTGGTTCAACTGCAGGGAGAGCTTTGA
AGAGTGTTGTGCAAGGAATTATATTGACTAGTGAAGCTGAGAAGCTTCATTCTATGAATTTGTTGCTTTATATGGCTCCG
TTGGCCGCGATGATTTTGTTGCCGGTTACTTTGTATATTGAAGGCAATGTGTTTGCGATAACGATTGAGAAAGCGAGGAG
TGATCCGTTTATTGTGTTTTTGTTGATTGGGAATGCTACTGTTGCTTATTTGGTGAATTTGACTAATTTTCTTGTGACTA
AGCATACTAGTGCTTTGACTCTTCAAGTTTTGGGGAATGCCAAAGCTGCTGTGGCTGCTGTTGTTTCGGTTTTGATATTC
AGAAATCCAGTTACTGTGATGGGGATGACTGGTTTTGGGATTACAATCATGGGTGTTGTGCTTTATAGTGAAGCTAAGAA
GAGATCTAAAGGTGCATCTCATTGA

Alignment

ORF - retro_mtru_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.76 %
• Parental protein coverage: 97.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DQKGSKTMKGASTRFFTIGLVAAWYSSNIGVLLLNKYLLSNYGFKYPIFLTMCHMTACSLFSYVAIAWMK
          DQ..............T....A.WY.SNIGVLLLNKYLLS.YG..YPIFLTM.HM..C...SY.AI....
Retrocopy DQRNNGSNINNNNLVTTSLIIASWYFSNIGVLLLNKYLLSFYGYRYPIFLTMLHMLSCAAYSYAAINVVQ

Parental  IVPMQTIRSRVQFFKISALSLIFCVSVVFGNISLRYLPVSFNQAIGATTPFFTAIFAYIMTFKREACLTY
          .VP.Q.I.S..QF.KI.ALS.IFC.SVV.GN.SLRYLPVSFNQAIGATTPFFTAIFA...T.K.E....Y
Retrocopy FVPYQQIHSKKQFLKIFALSAIFCFSVVCGNTSLRYLPVSFNQAIGATTPFFTAIFAFLITCKKETAEVY

Parental  LTLVPVVTGVVIASGGEPSFHLFGFIVCVAATAARALKSVLQGILLSSEGEKLNSMNLLLYMAPMAVVFL
          L.L.PVV.G.V.....EP.FHLFGF.VCV..TA.RALKSV.QGI.L.SE.EKL.SMNLLLYMAP.A...L
Retrocopy LALLPVVLGIVVSTNSEPLFHLFGFLVCVGSTAGRALKSVVQGIILTSEAEKLHSMNLLLYMAPLAAMIL

Parental  LPATLIMEENVVGITFALARDDTKIIWYLLFNSALAYFVNLTNFLVTKHTSALTLQVLGNAKGAVAVVVS
          LP.TL..E.NV..IT...AR.D..I...L..N...AY.VNLTNFLVTKHTSALTLQVLGNAK.AVA.VVS
Retrocopy LPVTLYIEGNVFAITIEKARSDPFIVFLLIGNATVAYLVNLTNFLVTKHTSALTLQVLGNAKAAVAAVVS

Parental  ILIFRNPVSVTGMMGYGLTVFGVILYSEAKKRTKG
          .LIFRNPV.V.GM.G.G.T..GV.LYSEAKKR.KG
Retrocopy VLIFRNPVTVMGMTGFGITIMGVVLYSEAKKRSKG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Medicago truncatula was not studied using RNA-Seq expression data.

ChIP-Seq

Medicago truncatula was not studied using ChIP-Seq data.

EST

Medicago truncatula was not studied using EST data.

TSS

Medicago truncatula was not studied using FANTOM5 data.

Lab

retro_mtru_1 was not experimentally validated.

Homology

Retrocopy orthology:

Medicago truncatula does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00080p00074790	1 retrocopy	retro_atri_6,
Medicago truncatula	MTR_3g070000	1 retrocopy	retro_mtru_1 ,
Solanum tuberosum	PGSC0003DMG401027186	1 retrocopy	retro_stub_37,
Prunus persica	PRUPE_ppa009115mg	1 retrocopy	retro_pper_41,
Solanum lycopersicum	Solyc05g052790.2	1 retrocopy	retro_slyc_35,
Theobroma cacao	TCM_042615	1 retrocopy	retro_tcac_6,
Vitis vinifera	VIT_13s0019g03270	1 retrocopy	retro_vvin_10,